Genes for regulating disease resistance in plants

ABSTRACT

Provided in the present invention are isolated nucleotide sequences encoding EDR1 proteins, the disruption of which is associated with enhanced disease resistance in plants. The invention also provides vectors comprising said nucleotide sequences.

This application claims priority to U.S. Provisional Application No. 60/135,895, filed May 26, 1999, the entirety of which is incorporated by reference herein.

Pursuant to 35 U.S.C. §202(c), it is acknowledged that the U.S. Government has certain rights in the invention described herein, which was made in part with funds from the National Institutes of Health, Grant No. GM46451.

FIELD OF THE INVENTION

This invention relates to the field of plant pathology and disease resistance. In particular, this invention relates to a novel gene and protein involved in the resistance of plants to various microbial pathogens.

BACKGROUND OF THE INVENTION

Various scientific and scholarly articles are referred to throughout the specification. These articles are incorporated by reference herein to describe the state of the art to which this invention pertains.

Plants defend themselves against pathogens through both pre-formed and inducible resistance mechanisms. Among the inducible responses are the hypersensitive resistance (HR) response and systemic acquired resistance (SAR). The HR is a localized plant response characterized by a suite of physiological changes culminating in plant cell death and cessation of pathogen growth. SAR is a systemic resistance response that is induced after formation of a necrotic lesion, either as part of the HR or as a symptom of disease. Although the HR and SAR have been the major forms of induced plant resistance studied, evidence for other resistance mechanisms exists.

The HR can be induced by the interaction between a plant resistance gene and a matching pathogen avirulence gene. Such “gene-for-gene” interactions provide a narrow range of resistance as they differentiate between races of a pathogen based on expression of a specific avirulence gene. Resistance gene products are thought to function as receptors for ligands produced directly or indirectly by avirulence genes. Multiple biochemical events are associated with the HR, including an oxidative burst, K/Cl ion exchange, deposition of autofluorescent compounds and callose in the cell wall, synthesis of antimicrobial phytoalexins, and cell death.

In Arabidopsis, SAR is associated with the expression of three pathogenesis-related genes: PR-1 (unknown function), BGL2 (β-glucanase, also known as PR-2) and PR-5 (a thaumatin-like protein). Arabidopsis mutants identified based upon constitutive expression of PR genes (cpr1 and cpr5) are resistant to the fungal pathogen Peronospora parasitica and the bacterial pathogen Pseudomonas syringae pv maculicola. Other mutants that constitutively express PR genes have been isolated based upon the development of spontaneous leaf lesions that are similar in appearance to the lesions of an HR. These lesion mimic mutants also show resistance to both fungal and bacterial pathogens.

Methyl jasmonate and ethylene may induce a defense pathway that is independent of SA. Wounding as well as pathogen attack induce the production of jasmonic acid, which in turn induces defense genes other than those associated with SAR, including genes that encode defensins and thionins. Defensins and thionins are low molecular weight polypeptides that have potent antimicrobial activity in vitro. Arabidopsis plants over-expressing endogenous thionin have increased resistance to the fungal pathogen Fusarium oxysporum. Transgenic Arabidopsis plants unable to accumulate SA and thus unable to express SAR are able to respond to the jasmonic acid signal and express both defensin and thionin genes. Mutants that constitutively express the proposed jasmonic acid pathway, but not the SA pathway have not been reported; however, the cpr5 and acd2 mutants of Arabidopsis constitutively expresses both PR genes and defensin.

Another defense pathway that is independent of SA is induced by the biocontrol bacterium P. fluorescens and is termed induced systemic resistance (ISR) (Pieterse, et al., 1996, Plant Cell 8:1225–1237). ISR is observed when Arabidopsis plants grown in soil containing P. fluorescens are challenged with virulent bacterial and fungal pathogens. Under these conditions, the Arabidopsis plants develop less severe disease symptoms than do control plants grown in soil alone. ISR is not associated with the expression of PR genes and is observed in plants unable to accumulate SA, indicating that this pathway is independent of SAR (Pieterse, et al., 1996, supra). It has not been determined whether the proposed jasmonic acid pathway contributes to ISR.

Screens for plant mutants that display enhanced resistance to virulent pathogens have been performed with several crop species. From these studies, barley resistant to powdery mildew (the mlo mutation), sugar-cane resistant to smut, mulberry resistant or tolerant to nematodes, mulberry resistant to Dogare disease and peppermint resistant to Verticillium wilt were identified. Of these, only the mlo resistance has been well characterized.

The mlo mutation of barley mediates resistance to all common races of the powdery mildew fungus Erysiphe graminis f sp hordei and, thus, provides a broader spectrum resistance than do the gene-for-gene type of resistance genes (Jorgensen, 1992, Euphytica 63:141–152).

Resistance in mlo mutants correlates with the formation of cell wall appositions that may prevent fungal penetration (Jorgensen, 1992, supra; Wolter et al., 1993, Mol. Gen. Genet. 239:122–128) and with plant cell death (Peterhänsel et al., 1997, Plant Cell 9:1397–1409). Defense genes are not constitutively expressed in mlo mutant barley; however, they are induced more rapidly upon infection by E. graminis (Peterhänsel, et al., 1997, supra). The wild-type Mlo gene has been cloned and is hypothesized to be a negative regulator of defense responses such that mutant mlo alleles mediate resistance by allowing abnormal defense responses to occur both spontaneously and during an E. g. hordei infection (Wolter, et al., 1993, supra; Buschges et al., 1997, Cell 88:695–705).

The isolation of novel mutants and genes that control defense responses will broaden the range of affected pathogens. It would be particularly advantageous to isolate mutants or genes involved in inducibly enhanced disease resistance without spontaneously occurring abnormal defense responses. Novel regulatory mutants are likely to have distinct pathogen ranges due to differential induction of unique subsets of genes. The different enhanced response may yield resistance responses that are spatially distinct (i.e. epidermal v. mesophyll cells), temporally distinct (i.e. affecting early v. late stages of infection), and/or comprised of a distinct subset of defense mechanisms (i.e. formation of necrotic lesions, deposition of callose, synthesis of antimicrobial Phytoalexins and others). The isolation of mutants will yield the critical gene(s), which can be used to transgenically transfer the enhanced resistance trait to new species.

SUMMARY OF THE INVENTION

Provided in the present invention is a novel gene (referred herein as EDR1), the disruption of which is associated with enhanced disease resistance in plants. The invention further provides transgenic plants and mutants having an enhanced resistance to plant pathogens. In these plants disease resistance is enhanced in a manner that does not involve constitutive expression of pathogenesis-related (PR) genes.

According to one aspect of the present invention, a disease resistance gene, EDR1, is provided. The EDR1 gene is located on Arabidopsis thaliana chromosome 1 between the ATEAT and NCC1 markers. The disruption of the EDR1 gene is associated with enhanced resistance to plant pathogens or other disease-causing agents. In a preferred embodiment, this gene encodes a protein with a kinase domain. In a more preferred embodiment, the gene contains exons that encode a protein that is 900–1000 amino acids in length. In a yet more preferred embodiment, the nucleic acid molecule contains an open reading frame that encodes a protein that is at least 50% identical over its full length to SEQ ID NO:2, and in a particularly preferred embodiment encodes SEQ ID NO:2. In a more particularly preferred embodiment, the nucleic acid molecule is comprised of SEQ ID NO:1.

Provided with this aspect of the invention is a cDNA molecule comprising the exons of the gene which encode a polypeptide 900–1000 amino acids in length. Also provided with this aspect of the invention is a nucleic acid molecule of at least 15 nucleotides in length, preferably at least 20 nucleotides in length, and most preferably at least 27 nucleotides in length, that is identical in sequence to a portion of the EDR1 gene located on Arabidopsis thaliana chromosome 1. In a preferred embodiment, the invention provides a nucleic acid molecule of at least 15, preferably 20, and most preferably 27 nucleotides in length, that is identical to or complementary to a consecutive 15, 20 or 27 nucleotide portion, respectively, of the sequence set out in SEQ ID NO:1.

According to another aspect of the invention an isolated nucleic acid is provided that is a plant gene and whose disruption is associated with enhanced resistance to plant pathogens or other disease-causing agents. This nucleic acid has a sequence that is selected from SEQ ID NOS:1, 5 or 9, a nucleic acid sequence that is at least 60% identical to SEQ ID NOS:1, 5 or 9 a nucleic acid encoding any of SEQ ID NOS:2, 4, 6 or 10, and a nucleic acid encoding a sequence that is at least 50% identical to any of SEQ ID NOS:2, 4, 6 or 10. Provided with this aspect of the invention is a polypeptide that is produced by the expression of the isolated nucleic acid molecule, and antibodies immunologically specific for the polypeptide. Also provided with this aspect of the invention is a nucleic acid molecule of, preferably, at least 27 nucleotides in length, more preferably, at least 20 nucleotides in length and, most preferably, 15 nucleotides in length that is identical in sequence to a consecutive 27, 20 or 15 base pair portion, respectively, of the sequence of the isolated nucleic acid molecule set forth above.

According to another aspect of the invention, a method is provided to enhance resistance of a plant to plant pathogens or other disease agents. This method comprises the removal of the EDR1 function from the plant cell. In a preferred embodiment, the removal of EDR1 function is accomplished by the addition of transgenes. The transgene preferably is comprised of at least 15 nucleotides of the gene on chromosome 1 of Arabidopsis thaliana. In a particularly preferred embodiment, the transgene expresses a mutant version of the EDR1 protein that interferes with the function of the native version of the protein (i.e., a “dominant negative” form). In a more particularly preferred embodiment, the nucleic acid is mutated in the portion encoding the kinase domain of EDR1. In a most preferred embodiment, the nucleic acid molecule is SEQ ID NO:1 and the coding sequence for residue 696 is mutated. In another more preferred embodiment, the transgene is comprised of at least 15 nucleotides of SEQ ID NO:1, sequences encoding SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6 or SEQ ID NO:7, or variants thereof. In a preferred embodiment, the transgene expresses the antisense strand of the nucleic acid molecule encoding EDR1. In another preferred embodiment, the transgene expresses the sense strand of the nucleic acid molecule. In a particularly preferred embodiment, transgenes express both the sense and anti-sense strands of the nucleic acid molecule. This aspect of the invention also provides a plant made from this method, and a reproductive unit from the plant, e.g., a seed. In a most preferred embodiment, the plant is Arabidopsis thaliana.

According to another aspect of the invention, a method is provided for screening plants for mutations conferring enhanced disease resistance by pathways that do not involve constitutive PR gene expression. The method comprises the following basic steps: (a) provide a plant variety and a pathogen to which the plant normally is not resistant; (b) inoculate a population of the plant variety with the pathogen; (c) select a sub-population of the plants that exhibit a disease-resistance response; and (d) eliminate from the sub-population any plants exhibiting constitutive PR gene expression.

The above method can be modified or optimized in a variety of ways, including, but not limited to: (1) using Arabidopsis as the plant for screening; most preferably using variety Col—O and the pathogen Pseudomonas syringae, to which Col—O is sensitive; (2) optionally, treating the plants (seeds) with a mutagenizing agent (such as fast-neutron bombardment, exposure to ethyl methanesulfonate, or exposure to gamma irradiation) prior to inoculation with the pathogen; (3) in the sub-population of plants exhibiting a disease resistance response, eliminating individuals exhibiting a hypersensitive response (HR); and (4) challenging the selected resistant plants to other plant pathogens to further select for broad spectrum resistance. In the last instance, it is particularly preferred to determine whether the selected resistant plants are resistant to several classes of plant pathogens. Accordingly, if the initial pathogen used in the screen was a bacterium, for example, the secondary screen might be against a fungal or viral pathogen.

According to another aspect of the invention, mutant Arabidopsis plants produced by the above-described method are provided. In preferred embodiments, mutants edr1, edr2, edr3 and edr4 are provided. These mutants each comprise mutations in different genes, the mutations resulting in the plants' enhanced disease resistance. In another preferred embodiment, the wild-type genes, EDR1 (described in greater detail below), EDR2, EDR3 and EDR4, corresponding to the mutated genes in the aforementioned edr1, edr2, edr3 and edr4 Arabidopsis mutants, respectively, are also provided.

Other features and advantages of the present invention will be better understood by reference to the drawings, detailed description and examples that follow.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Response of edr1 plants to P. syringae. Arabidopsis plants were vacuum infiltrated with P. syringae and bacterial growth in plant leaves monitored over 4 days. Data points represent the mean±SE of three samples. Each graph is representative of at least three experiments. FIG. 1A. Time course of P.s. tomato DC3000 growth in Arabidopsis leaves. FIG. 1B. Time course of P.S. maculicola M4 growth in Arabidopsis leaves.

FIG. 2. Alignment of the Arabidopsis EDR1 and CTR1 proteins. SEQ ID NO: 2, representing EDR1 amino acid sequence, and SEQ ID NO: 3, representing CTR1 amino acid sequence were aligned using the GCG GAP program with a gap creation penalty of 12 and a gap extension penalty of 2. Vertical bars indicate amino acid identities, dots indicate functionally similar amino acids. The highly similar region from residue 668 to the end of SEQ ID NO: 2 (residue 933) corresponds to the kinase domain.

FIG. 3. Alignment of Arabidopsis EDR1 and tomato TCTR2 predicted amino acid sequences. SEQ ID NO: 2 represents EDR1 amino acid sequence, and SEQ ID NO: 4 represents TCTR2 amino acid sequence.

FIG. 4. Alignment of the kinase domains of the Arabidopsis EDR1 (SEQ ID NO: 2), TCTR2 (SEQ ID NO: 4), Rice EDR1 (SEQ ID NO: 6), and a Arabidopsis CTR1 (SEQ ID NO: 3) proteins. Black boxes indicate identical amino acids. Arrows indicate regions that distinguish CTR1 from the other three genes. These regions can be used to develop PCR primers that will specifically amplify EDR1-homologous genes from both monocot and dicot species.

DETAILED DESCRIPTION OF THE INVENTION

I. Definitions

Various terms relating to the biological molecules of the present invention are used hereinabove and also throughout the specifications and claims.

With respect to the genotypes of the invention, the terms “EDR1” and “edr1” are used. The term “EDR1” is used to designate the naturally-occurring or wild-type genotype. This genotype has the phenotype of naturally-occurring spectrum of disease resistance and susceptibility. The term “edr1” refers to a genotype having recessive mutation(s) in the wild-type EDR1 gene. The phenotype of edr1 individuals is enhanced disease resistance. Where used hereinabove and throughout the specifications and claims, the term “EDR1” refers to the protein product of the EDR1 gene.

In reference to the mutant plants of the invention, the term “null mutant” is used to designate an organism or genomic DNA sequence with a mutation that causes the product of the EDR1 gene to be non-functional or largely absent. Such mutations may occur in the coding and/or regulatory regions of the EDR1 gene, and may be changes of individual residues, or insertions or deletions of regions of nucleic acids. These mutations may also occur in the coding and/or regulatory regions of other genes which may regulate or control the EDR1 gene and/or the product of the EDR1 gene so as to cause said gene product to be non-functional or largely absent.

With reference to nucleic acids of the invention, the term “isolated nucleic acid” is sometimes used. This term, when applied to genomic DNA, refers to a DNA molecule that is separated from sequences with which it is immediately contiguous (in the 5′ and 3′ directions) in the naturally-occurring genome of the organism from which it was derived. For example, the “isolated nucleic acid” may comprise a DNA molecule inserted into a vector, such as a plasmid or virus vector, or integrated into the genomic DNA of a procaryote or eukaryote. An “isolated nucleic acid molecule” may also comprise a cDNA molecule or a synthetic DNA molecule.

With respect to RNA molecules, the term “isolated nucleic acid” primarily refers to an RNA molecule encoded by an isolated DNA molecule as defined above. Alternatively, the term may refer to an RNA molecule that has been sufficiently separated from RNA molecules with which it would be associated in its natural state (i.e., in cells or tissues), such that it exists in a “substantially pure” form.

Nucleic acid sequences and amino acid sequences can be compared using computer programs that align the similar sequences of the nucleic or amino acids thus define the differences. For purposes of this invention, the GAP program from the GCG Wisconsin Package Version 9.1 (available from the “Genetics Computer Group”, Madison, Wis.) with a gap creation penalty of 12 and a gap extension penalty of 2 is used herein to compare sequence identity and similarity.

The term “substantially the same” refers to nucleic acid or amino acid sequences having sequence variations that do not materially affect the nature of the protein (i.e. the structure, thermostability characteristics and/or biological activity of the protein). With particular reference to nucleic acid sequences, the term “substantially the same” is intended to refer to the coding region and to conserved sequences governing expression, and refers primarily to degenerate codons encoding the same amino acid, or alternate codons encoding conservative substitute amino acids in the encoded polypeptide. With reference to amino acid sequences, the term “substantially the same” refers generally to conservative substitutions and/or variations in regions of the polypeptide not involved in determination of structure or function.

The terms “percent identical” and “percent similar” are also used herein in comparisons among amino acid and nucleic acid sequences. When referring to amino acid sequences, “percent identical” refers to the percent of the amino acids of the subject amino acid sequence that have been matched to identical amino acids in the compared amino acid sequence by a sequence analysis program. “Percent similar” refers to the percent of the amino acids of the subject amino acid sequence that have been matched to identical or conserved amino acids. Conserved amino acids are those which differ in structure but are similar in physical properties such that the exchange of one for another would not appreciably change the tertiary structure of the resulting protein. Conservative substitutions are defined in Taylor (1986, J. Theor. Biol. 119:205). When referring to nucleic acid molecules, “percent identical” refers to the percent of the nucleotides of the subject nucleic acid sequence that have been matched to identical nucleotides by a sequence analysis program.

With respect to protein, the term “isolated protein” or “isolated and purified protein” is sometimes used herein. This term refers primarily to a protein produced by expression of an isolated nucleic acid molecule of the invention. Alternatively, this term may refer to a protein which has been sufficiently separated from other proteins with which it would naturally be associated, so as to exist in “substantially pure” form.

With respect to antibodies of the invention, the terms “immunologically specific”, “immunospecific” or “specific” refer to antibodies that bind to one or more epitopes of a protein of interest, but which do not substantially recognize and bind other molecules in a sample containing a mixed population of antigenic biological molecules.

With respect to oligonucleotides, but not limited thereto, the term “specifically hybridizing” refers to the association between two single-stranded nucleotide molecules of sufficiently complementary sequence to permit such hybridization under pre-determined conditions generally used in the art (sometimes termed “substantially complementary”). In particular, the term refers to hybridization of an oligonucleotide with a substantially complementary sequence contained within a single-stranded DNA or RNA molecule of the invention, to the substantial exclusion of hybridization of the oligonucleotide with single-stranded nucleic acids of non-complementary sequence.

The term “promoter region” refers generally to the transcriptional regulatory regions of a gene, which may be found at the 5′ or 3′ side of the coding region, or within the coding region, or within introns.

The term “reporter gene” refers to genetic sequences which may be operably linked to a promoter region forming a transgene, such that expression of the reporter gene coding region is regulated by the promoter and expression of the transgene is readily assayed. The term “selectable marker gene” refers to a gene product which when expressed confers a selectable phenotype, such as antibiotic resistance, on a transformed cell or plant. The term “operably linked” means that the regulatory sequences necessary for expression of the coding sequence are placed in the DNA molecule in the appropriate positions relative to the coding sequence so as to effect expression of the coding sequence. This same definition is sometimes applied to the arrangement of coding sequences and transcription control elements (e.g. promoters, enhancers, and termination elements) in an expression vector.

The term “DNA construct” refers to genetic sequences used to transform plants or other organisms (e.g., bacteria, yeast). When transforming plants, these constructs may be administered to plants in a viral or plasmid vector. Other methods of delivery such as Agrobacterium T-DNA mediated transformation and transformation using the biolistic process are also contemplated to be within the scope of the present invention. The transforming DNA may be prepared according to standard protocols such as those set forth in “Current Protocols in Molecular Biology”, eds. Frederick M. Ausubel et al., John Wiley & Sons, 2000.

II. Description

In accordance with the present invention, a gene is provided that is a novel regulator of plant disease resistance. This gene, EDR1, was initially isolated from Arabidopsis thaliana. Its manner of regulating disease resistance is novel and surprising. When the functional product of the gene is eliminated, the plants exhibit enhanced disease resistance, but without infection the plants do not exhibit constitutive expression of the pathogenesis-related genes or spontaneous necrotic lesions. Additionally, the induction of the pathogenesis-related genes and the halting of pathogen growth occurs later after infection than observed with other inducible disease defense responses.

The EDR1 gene was first isolated in a mutated form (edr1) from libraries of mutagenized Arabidopsis seed. The edr1 mutant was isolated firstly because of its enhanced resistance to the pathogenic bacterium Pseudomonas syringae tomato DC3000. Secondly, the edr1 mutant was selected because it did not have constitutive expression of the PR-1 gene.

Additionally, the edr1 mutant was found to have reduced susceptibility to Pseudomonas syringae maculicola M4 and the powdery mildew fungus Erysiphe cichoracearum. The expression of the SAR-related genes, PR-1, PR-5 and BGL2, was not detectable prior to inoculation with E. cichoracearum, indicating that the edr1 mutant does not function by way of constitutive stimulation of the SAR pathway. Three days after infection, the PR-1 message was four times higher in the mutant than wildtype plants, indicating that the mutant displays stronger induction of the SAR pathway in response to normally virulent pathogens than does the wild-type plant.

The enhanced disease resistance of the edr1 mutant segregates as a recessive trait. Genetic linkage analysis establishes that the EDR1 gene is located on chromosome 1, 3.2 centiMorgans centromeric from the SSLP (simple sequence length polymorphism) marker ATEAT1 and 0.85 centiMorgans telomeric from the CAPS (co-dominant amplified polymorphic sequence) marker NCC1.

The EDR1 gene was isolated using a positional cloning approach. Two overlapping bacterial artificial chromosome (BAC) clones containing Arabidopsis genomic DNA were identified that contained closely-linked molecular markers. Sequence information from the Arabidopsis Genome Project was used to create additional molecular markers and allowed the EDR1 gene to be mapped to a 100 kb interval. Sequence analysis of this 100 kb region revealed 25 potential protein coding genes. Candidate genes were sequenced from the edr1 mutant and compared to the known wildtype sequence. Upon sequencing a gene with similarity to MAP3 kinases (also known as “mitogen activated protein kinase kinase kinase”), a single nucleotide difference was found that produces a premature stop codon, thereby truncating the C-terminal half of the protein containing the kinase domain. This null mutation fits well with the recessive nature of the edr1 mutation and this MAP3 kinase gene co-segregates with the EDR1 gene, therefore this MAP3 kinase gene is referred to as the EDR1 gene (a cDNA is SEQ ID NO:1 and the genomic clone is found on BAC F22013, Genbank AC003981, and in Genbank at No. AAC14047.1). The EDR1 predicted protein (SEQ ID NO:2) is 933 amino acids long and contains a “kinase domain” from residues 668 to 933 (Hanks et al., 1988, Science 241:42–52).

Although the EDR1 genomic clone and cDNA from Arabidopsis thaliana are described and exemplified herein, this invention is intended to encompass nucleic acid sequences and proteins from other plants that are sufficiently similar to be used instead of the Arabidopsis EDR1 nucleic acid and proteins for the purposes described below. These include, but are not limited to, allelic variants and natural mutants of SEQ ID NO:1, which are likely to be found in different species of plants or varieties of Arabidopsis. Because such variants are expected to possess certain differences in nucleotide and amino acid sequence, this invention provides an isolated EDR1 nucleic acid molecule having at least about 50% (preferably 60%, more preferably 70% and even more preferably over 80%) sequence identity in the coding regions with the nucleotide sequence set forth as SEQ ID NO:1 (and, most preferably, specifically comprising the coding region of SEQ ID NO:1). This invention also provides isolated polypeptide products of SEQ ID NO:1, having at least about 50% (preferably 60%, 70%, 80% or greater) sequence identity with the amino acid sequences of SEQ ID NO:2. Because of the natural sequence variation likely to exist among EDR1 genes, one skilled in the art would expect to find up to about 30–40% nucleotide sequence variation, while still maintaining the unique properties of the EDR1 gene and encoded polypeptide of the present invention. Such an expectation is due in part to the degeneracy of the genetic code, as well as to the known evolutionary success of conservative amino acid sequence variations, which do not appreciably alter the nature of the encoded protein. Accordingly, such variants are considered substantially the same as one another and are included within the scope of the present invention.

Many diverse kinases are involved the signal transduction pathways; however, the kinase domain is highly conserved in all kinases. The EDR1 protein sequence contains regions of high similarity to a large number of protein kinases. The functional specialization that allows these kinases to operate in specific signal transduction pathways lies both in the kinase domain and non-kinase domains. The Arabidopsis CTR1 kinase protein (SEQ ID NO:3) displays moderate similarity to EDR1 (40% identity, 49% similarity). While the similarity is highest in the putative kinase domain (residues 668–933 of SEQ ID NO:2), it extends to the rest of the protein as well (FIG. 2) suggesting a possible similarity of specialization. CTR1 is a negative regulator of the ethylene response pathway (Kieber, 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol. 48:277–296). By analogy, EDR1 may function as a negative regulator of specific defense response pathways.

EDR1 genes have been identified in crop plants by their extensive homology to EDR1 outside the kinase region. The tomato TCTR2 predicted protein sequence (SEQ ID NO:4) shows extensive homology throughout the protein sequence (55% identity, 61% similarity) (FIG. 3). TCTR2 is more similar to EDR1 than CTR1 is to EDR1, both inside and outside the kinase region (Table 1), but the high similarity outside the kinase region in particular indicates that they are homologous proteins.

EDR1 also shows a high similarity to a gene product from rice (SEQ ID NOS:5 and 6 for the cDNA and predicted amino acid sequences, respectively). The amino acid sequence encoded by this rice gene is 85% identical to EDR1 in the kinase domain. This high degree of identity is comparable to the TCTR2-EDR1 identity of 86% in the kinase region, indicating that the rice gene is also part of an EDR1 gene family.

TABLE 1 Comparison of amino acid sequences EDR1 to CTR1, TCTR2 and Rice EDR. CTR1 TCTR2 RICE EDR Region I (1–667 aa) Identity 25% 43% — Similarity 32% 49% — Region II - Kinase (668–933 aa) Identity 65% 86% 85% Similarity 74% 90% 88%

An EDR1 homolog from barley also has been identified. A cDNA sequence corresponding to the barley EDR1 homolog and its predicted amino acid sequence are set forth herein as SEQ ID NO:9 and SEQ ID NO:10, respectively.

The present invention encompasses these EDR1 genes from tomato, rice and barley, as well as TCTR2. The isolation of four EDR1 genes enables the isolation of additional EDR1 genes. The known EDR1 genes encompass both monocots and dicots and therefore are excellent candidates for determining conserved amino acid sequences that can be used as probes to identify new EDR1 genes from the entire plant kingdom. The sequences on which to base such probes are indicated by arrows in FIG. 4, however many other sequences are present that would be equally as appropriate. The criteria for selecting probe sequence is that they should be well conserved among the EDR1 homologs EDR1, TCTR2 and the rice and barley EDR1, but not conserved in the general kinase CTR1, and therefore will only identify EDR1 homologous kinases. Indeed, the utility of this strategy was proven by the identification of the barley EDR1 gene, using two degenerate oligonucleotides corresponding to the amino acid sequences indicated by the arrows in FIG. 4 (SEQ ID NOS: 7 and 8). These primers were used to amplify the intervening region of EDR1 homologs from barley using cDNA as a template. The PCR products were then cloned and sequenced, revealing several identical clones that were over 90% identical to the rice EDR1 sequence. To obtain the full length cDNA sequence of this gene, 5′ and 3′ RACE (“rapid amplification of cDNA ends”) PCR was performed.

The edr1 mutant from Arabidopsis is also part of the present invention. It exhibits an enhanced disease resistance with characteristics of regulation that have not been previously observed. This mutant is novel in its ability to poise the plant metabolism for a heightened disease-resistance response without the constitutive induction of the pathogenesis-related genes and non-infection related necrotic lesions on leaf tissue.

Furthermore, upon infection, the pathogenesis-related genes are induced much later than currently known disease resistance mutants, resulting in a halting of pathogen growth at a later stage of infection. This distinction is useful because the enhanced disease resistance pathways exhibited by edr1 mutants of this invention are not constitutive in the uninfected plant, and so do not cause death of tissue vital for photosynthesis until the plant is actually challenged with a pathogen. Additionally, the edr1 mutants may well be effective against a spectrum of diseases because they are active against a later infection stage. Due to the unique phenotype conferred by the edr1 mutation, it is easy to screen populations of mutagenized plants and obtain other edr1 mutants. Such edr1 mutants from all other species of plants are considered to be within the scope of this invention.

It is contemplated that the present invention encompasses not only other plant homologs of the EDR1 gene, but also using these homologs to engineer enhanced disease resistance in other plant species. The edr1 mutant establishes that null mutations in this gene result in plants with enhanced disease resistance. Once the EDR1 homolog of a specific species is isolated, established methods exist to create transgenic plants that are deficient in the EDR1 gene product. These edr1-like transgenic plants are also considered part of the invention.

The following sections set forth the general procedures involved in practicing the present invention. To the extent that specific materials are mentioned, it is merely for purposes of illustration and is not intended to limit the invention. Unless otherwise specified, general cloning procedures, such as those set forth in Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory (1989) (hereinafter “Sambrook et al.”) or Ausubel et al. (eds) Current Protocols in Molecular Biology, John Wiley & Sons (2000) (hereinafter “Ausubel et al.”) are used.

III. Preparation of edr1 Mutants, EDR1 Nucleic Acids, Proteins, Antibodies and Transgenic Plants.

A. Isolation of EDR1 Genetic Mutants

Populations of plant mutants are available from which edr1 mutants in other plant species can be isolated. Many of these populations are very likely to contain plants with null mutations in the EDR1 gene. Such populations can be made by chemical mutagenesis, radiation mutagenesis, and transposon or T-DNA insertions. The methods to make mutant populations are well known in the art.

The nucleic acids of the invention can be used to isolate edr1 mutants in other species. In species such as maize where transposon insertion lines are available, oligonucleotide primers can be designed to screen lines for insertions in the EDR1 gene. Plants with transposon or T-DNA insertions in the EDR1 gene are very likely to have lost the function of the gene product. Through breeding, a plant line may then be developed that is homozygous for the non-functional copy of the EDR1 gene. The PCR primers for this purpose are designed so that a large portion of the coding sequence the EDR1 gene are specifically amplified using the sequence of the EDR1 gene from the species to be probed (see Baumann et al., 1998, Theor. Appl. Genet. 97:729–734).

Other edr1-like mutants can easily be isolated from mutant populations using the distinctive phenotype characterized in accordance with the present invention. This approach is particularly appropriate in plants with low ploidy numbers where the phenotype of a recessive mutation is more easily detected. In order to identify these mutants, the population of plants would be inoculated with a strain of powdery mildew, for example Erysiphe cichoracearum or E. cruciferarum strain UEA1. After a suitable period of incubation (e.g., 5–10 days), plants would then be screened for phenotype of the edr1 mutant: the development of distinct necrotic and collapsed regions on the leaves. That the phenotype is caused by an edr1 mutation is then established by molecular means well known in the art. Species contemplated to be screened with this approach include but are not limited to: aster, barley, begonia, beet, cantaloupe, carrot, chrysanthemum, clover, corn, cucumber, delphinium, grape, lawn and turf grasses, lettuce, pea, peppermint, rice, rutabaga, sugar beet, tomatillo, tomato, turnip, wheat, and zinnia.

B. Isolation of EDR1 Genes

A gene can be defined by its mapped position in the plant genome. Although the chromosomal position of the gene can change dramatically, the position of the gene in relation to its neighbor genes is often highly conserved (Lagercrantz et al., 1996, Plant J. 9:13–20). This conserved micro-colinearity can be used to isolate the EDR1 gene from distantly related plant species. In accordance with the present invention, the screening of genes and markers that flank EDR1 on the chromosome are known and are further present on the BAC clone of the Arabidopsis genome (BAC F22013, Genbank locus AC003981). These genes and markers can be used to isolate the EDR1 gene in their midst, or to confirm the identity of an isolated EDR1 nucleic acid (described below). For example, the various coding sequences can be used to design probes to isolate the EDR1 gene on BAC clones or to map the chromosomal location of the EDR1 gene using recombination frequencies. Additionally, genes highly homologous to those on Arabidopsis BAC F22013 are already known in other species, and these homologous genes may be used to locate EDR1 in these genomes. There are several versions of these procedures, and all will be well known to those skilled in the art.

C. Isolation of EDR1 Nucleic Acid Molecules

Nucleic acid molecules encoding the EDR1 protein may be isolated from Arabidopsis or any other plant of interest using methods well known in the art. Nucleic acid molecules from Arabidopsis may be isolated by screening Arabidopsis cDNA or genomic libraries with oligonucleotides designed to match the Arabidopsis nucleic acid sequence of EDR1 gene (SEQ ID NO:1). In order to isolate EDR1-encoding nucleic acids from plants other than Arabidopsis, oligonucleotides designed to match the nucleic acids encoding the Arabidopsis EDR1 protein may be likewise used with cDNA or genomic libraries from the desired species. If the EDR1 gene from a species is desired, the genomic library is screened. Alternately, if the protein coding sequence is of particular interest, the cDNA library is screened. In positions of degeneracy, where more than one nucleic acid residue could be used to encode the appropriate amino acid residue, all the appropriate nucleic acids residues may be incorporated to create a mixed oligonucleotide population, or a neutral base such as inosine may be used. The strategy of oligonucleotide design is well known in the art (see also Sambrook et al.).

Alternatively, PCR (polymerase chain reaction) primers may be designed by the above method to encode a portion of the Arabidopsis EDR1 protein, and these primers used to amplify nucleic acids from isolated cDNA or genomic DNA. In a preferred embodiment, the oligonucleotides used to isolate EDR1 nucleic acids are designed to encode sequences conserved in Arabidopsis EDR1 (SEQ ID NO:2), tomato TCTR2 (SEQ ID NO:4), rice EDR1 (SEQ ID NO:6), and barley EDR1 (SEQ ID NO:10), but not Arabidopsis CTRL (SEQ ID NO:3). In a particularly preferred embodiment, the sequences marked by arrows on FIG. 4, AVKKFLDQD and DPNLRPSFA (SEQ ID NOS:7 and 8) are used to design oligonucleotides and probes.

In accordance with the present invention, nucleic acids having the appropriate sequence homology with an Arabidopsis EDR1 nucleic acid molecule may be identified by using hybridization and washing conditions of appropriate stringency. For example, hybridizations may be performed, according to the method of Sambrook et al. (1989, supra), using a hybridization solution comprising: 5×SSC, 5× Denhardt's reagent, 1.0% SDS, 100 μg/ml denatured, fragmented salmon sperm DNA, 0.05% sodium pyrophosphate and up to 50% formamide. Hybridization is carried out at 37–42° C. for at least six hours. Following hybridization, filters are washed as follows: (1) 5 minutes at room temperature in 2×SSC and 1% SDS; (2) 15 minutes at room temperature in 2×SSC and 0.1% SDS; (3) 30 minutes–1 hour at 37° C. in 1×SSC and 1% SDS; (4) 2 hours at 42–65° in 1×SSC and 1% SDS, changing the solution every 30 minutes.

One common formula for calculating the stringency conditions required to achieve hybridization between nucleic acid molecules of a specified sequence homology (Sambrook et al., 1989, supra) is: T _(m)=81.5° C.+16.6Log [Na+]+0.41(% G+C)−0.63 (% formamide)−600/#bp in duplex

As an illustration of the above formula, using [N+]=[0.368] and 50% formamide, with GC content of 42% and an average probe size of 200 bases, the T_(m) is 57° C. The T_(m) of a DNA duplex decreases by 1–1.5° C. with every 1% decrease in homology. Thus, targets with greater than about 75% sequence identity would be observed using a hybridization temperature of 42° C. In a preferred embodiment, the hybridization is at ˜37° C. and the final wash is at 42° C., in a more preferred embodiment the hybridization is at 42° and the final wash is at 50°, and in a most preferred embodiment the hybridization is at 42° C. and final wash is at 65° C., with the above hybridization and wash solutions. Conditions of high stringency include hybridization at 42° C. in the above hybridization solution and a final wash at 65° C. in 0.1×SSC and 0.1% SDS for 10 minutes.

Nucleic acids of the present invention may be maintained as DNA in any convenient cloning vector. In a preferred embodiment, clones are maintained in plasmid cloning/expression vector, such as pBluescript (Stratagene, La Jolla, Calif.), which is propagated in a suitable E. coli host cell.

Arabidopsis EDR1 nucleic acid molecules of the invention include DNA, RNA, and fragments thereof which may be single- or double-stranded. Thus, this invention provides oligonucleotides (sense or antisense strands of DNA or RNA) having sequences capable of hybridizing with at least one sequence of a nucleic acid molecule encoding the protein of the present invention. Such oligonucleotides are useful as probes for detecting Arabidopsis EDR1 genes or transcripts.

D. Engineering Plants to Alter EDR1 Activity

While the edr1 null mutant of the present invention is a naturally occurring mutant, any plant may be transgenically engineered to display a similar phenotype. While the natural edr1 mutant has lost the functional product of the EDR1 gene due to a premature stop codon in its coding sequence, a transgenic plant can be made that also has a similar loss of the EDR1 product. This approach is particularly appropriate to plants with high ploidy numbers, including but not limited to wheat.

A synthetic null mutant can be created by a expressing a mutant form of the EDR1 protein to create a “dominant negative effect”. While not limiting the invention to any one mechanism, this mutant EDR1 protein will compete with wild-type EDR1 protein for interacting proteins in a transgenic plant. By over-producing the mutant form of the protein, the signaling pathway used by the wild-type EDR1 protein can be effectively blocked. Examples of this type of “dominant negative” effect are well known for both insect and vertebrate systems (Radke et al, 1997, Genetics 145:163–171; Kolch et al., 1991, Nature 349:426–428). In a preferred embodiment, the mutant protein is produced by mutating the coding sequence corresponding to several residues in the kinase domain of EDR1 (amino acids 750–1015, Hanks et al., 1988, Science 241:42–52). In a particularly preferred embodiment, the coding sequence corresponding to the lysine residue at position 778 of SEQ ID NO:2 (which is conserved in all known kinases and required for kinase function) is mutated to code for a different, preferably non-similar, amino acid residue.

A second kind of synthetic null mutant can be created by inhibiting the translation of the EDR1 mRNA by “post-transcriptional gene silencing”. The EDR1 gene from the species targeted for down-regulation, or a fragment thereof, may be utilized to control the production of the encoded protein. Full-length antisense molecules can be used for this purpose. Alternatively, antisense oligonucleotides targeted to specific regions of the EDR1-encoded RNA that are critical for translation may be utilized. The use of antisense molecules to decrease expression levels of a pre-determined gene is known in the art. Antisense molecules may be provided in situ by transforming plant cells with a DNA construct which, upon transcription, produces the antisense RNA sequences. Such constructs can be designed to produce full-length or partial antisense sequences. This gene silencing effect can be enhanced by transgenically over-producing both sense and antisense RNA of the gene coding sequence so that a high amount of dsRNA is produced (for example see Waterhouse et al., 1998, PNAS 95:13959–13964). In a preferred embodiment, part or all of the EDR1 coding sequence antisense strand is expressed by a transgene. In a particularly preferred embodiment, hybridizing sense and antisense strands of part or all of the EDR1 coding sequence are transgenically expressed.

A third type of synthetic null mutant can also be created by the technique of “co-suppression”. Plant cells are transformed with a copy of the endogenous gene targeted for repression. In many cases, this results in the complete repression of the native gene as well as the transgene. In a preferred embodiment, the EDR1 gene from the plant species of interest is isolated and used to transform cells of that same species.

Transgenic plants displaying enhanced EDR1 activity can also be created. This is accomplished by transforming plant cells with a transgene that expresses part of all of an EDR1 coding sequence, or a sequence that encodes the either the EDR1 protein or a protein functionally similar to it. In a preferred embodiment, the complete EDR1 coding sequence is transgenically over-expressed. In a particularly preferred embodiment, the coding sequence corresponding to the kinase domain of EDR1 is over-expressed.

Transgenic plants with one of the transgenes mentioned above can be generated using standard plant transformation methods known to those skilled in the art. These include, but are not limited to, Agrobacterium vectors, polyethylene glycol treatment of protoplasts, biolistic DNA delivery, UV laser microbeam, gemini virus vectors, calcium phosphate treatment of protoplasts, electroporation of isolated protoplasts, agitation of cell suspensions in solution with microbeads coated with the transforming DNA, agitation of cell suspension in solution with silicon fibers coated with transforming DNA, direct DNA uptake, liposome-mediated DNA uptake, and the like. Such methods have been published in the art. See, e.g., Methods for Plant Molecular Biology (Weissbach & Weissbach, eds., 1988); Methods in Plant Molecular Biology (Schuler & Zielinski, eds., 1989); Plant Molecular Biology Manual (Gelvin, Schilperoort, Verma, eds., 1993); and Methods in Plant Molecular Biology—A Laboratory Manual (Maliga, Klessig, Cashmore, Gruissem & Varner, eds., 1994).

The method of transformation depends upon the plant to be transformed. Agrobacterium vectors are often used to transform dicot species. Agrobacterium binary vectors include, but are not limited to, BIN19 (Bevan, 1984) and derivatives thereof, the pBI vector series (Jefferson et al., 1987), and binary vectors pGA482 and pGA492 (An, 1986) For transformation of monocot species, biolistic bombardment with particles coated with transforming DNA and silicon fibers coated with transforming DNA are often useful for nuclear transformation.

DNA constructs for transforming a selected plant comprise a coding sequence of interest operably linked to appropriate 51 (e.g., promoters and translational regulatory sequences) and 3′ regulatory sequences (e.g., terminators). In a preferred embodiment, the coding region is placed under a powerful constitutive promoter, such as the Cauliflower Mosaic Virus (CaMV) 35S promoter or the figwort mosaic virus 35S promoter. Other constitutive promoters contemplated for use in the present invention include, but are not limited to: T-DNA mannopine synthetase, nopaline synthase (NOS) and octopine synthase (OCS) promoters.

Transgenic plants expressing a sense or antisense EDR1 coding sequence under an inducible promoter are also contemplated to be within the scope of the present invention. Inducible plant promoters include the tetracycline repressor/operator controlled promoter, the heat shock gene promoters, stress (e.g., wounding)-induced promoters, defense responsive gene promoters (e.g. phenylalanine ammonia lyase genes), wound induced gene promoters (e.g. hydroxyproline rich cell wall protein genes), chemically-inducible gene promoters (e.g., nitrate reductase genes, glucanase genes, chitinase genes, etc.) and dark-inducible gene promoters (e.g., asparagine synthetase gene) to name a few.

Tissue specific and development-specific promoters are also contemplated for use in the present invention. Examples of these included, but are not limited to: the ribulose bisphosphate carboxylase (RuBisCo) small subunit gene promoters or chlorophyll a/b binding protein (CAB) gene promoters for expression in photosynthetic tissue; the various seed storage protein gene promoters for expression in seeds; and the root-specific glutamine synthetase gene promoters where expression in roots is desired.

The coding region is also operably linked to an appropriate 3′ regulatory sequence. In a preferred embodiment, the nopaline synthetase polyadenylation region (NOS) is used. Other useful 3′ regulatory regions include, but are not limited to the octopine (OCS) polyadenylation region.

Using an Agrobacterium binary vector system for transformation, the selected coding region, under control of a constitutive or inducible promoter as described above, is linked to a nuclear drug resistance marker, such as kanamycin resistance. Other useful selectable marker systems include, but are not limited to: other genes that confer antibiotic resistances (e.g., resistance to hygromycin or bialaphos) or herbicide resistance (e.g., resistance to sulfonylurea, phosphinothricin, or glyphosate).

Plants are transformed and thereafter screened for one or more properties, including the lack of EDR1 protein, EDR1 mRNA, or enhanced resistance to plant pathogens, in particular powdery mildew fungi, the Erysiphe spp., and most particularly E. cichoracearum and E. cruciferarum. It should be recognized that the amount of expression, as well as the tissue-specific pattern of expression of the transgenes in transformed plants can vary depending on the position of their insertion into the nuclear genome. Such positional effects are well known in the art. For this reason, several nuclear transformants should be regenerated and tested for expression of the transgene.

Transgenic plants that exhibit one or more of the aforementioned desirable phenotypes can be used for plant breeding, or directly in agricultural or horticultural applications. Plants containing one transgene may also be crossed with plants containing a complementary transgene in order to produce plants with enhanced or combined phenotypes.

E. In Vivo Synthesis of the EDR1 Protein

The availability of amino acid sequence information, such as the full length sequence in SEQ ID NO: 2, enables the preparation of a synthetic gene that can be used to synthesize the Arabidopsis EDR1 protein in standard in vivo expression systems, or to transform different plant species. The sequence encoding Arabidopsis EDR1 from isolated native nucleic acid molecules can be utilized. Alternately, an isolated nucleic acid that encodes the amino acid sequences of the invention can be prepared by oligonucleotide synthesis. Codon usage tables can be used to design a synthetic sequence that encodes the protein of the invention. In a preferred embodiment, the codon usage table has been derived from the organism in which the synthetic nucleic acid will be expressed. For example, the codon usage for pea (Pisum sativum) would be used to design an expression DNA construct to produce the Arabidopsis EDR1 in pea. Synthetic nucleic acid molecules may be prepared by the phosphoramadite method employed in the Applied Biosystems 38A DNA Synthesizer or similar devices, and thereafter may be cloned and amplified in an appropriate vector.

The availability of nucleic acids molecules encoding the Arabidopsis EDR1 enables production of the protein using in vivo expression methods known in the art. According to a preferred embodiment, the protein may be produced by expression in a suitable expression system. The EDR1 protein of the present invention may also be prepared by in vitro transcription and translation of either native or synthetic nucleic acid sequences that encode the proteins of the present invention. While in vitro transcription/translation is not the method of choice for preparing large quantities of the protein, it is ideal for preparing small amounts of native or mutant proteins for research purposes, particularly since in vitro methods allow the incorporation of radioactive nucleotides such as ³⁵S-labeled methionine. The EDR1 proteins of the present invention may be prepared by various synthetic methods of peptide synthesis via condensation of one or more amino acid residues, in accordance with conventional peptide synthesis methods. The EDR1 produced by native cells or by gene expression in a recombinant procaryotic or eukaryotic system may be purified according to methods known in the art.

F. Antibodies Immunospecific for EDR1

The present invention also provides antibodies that are immunologically specific to the Arabidopsis EDR1 of the invention. Polyclonal antibodies may be prepared according to standard methods. In a preferred embodiment, monoclonal antibodies are prepared, which are specific to various epitopes of the protein. Monoclonal antibodies may be prepared according to general methods of Köhler and Milstein, following standard protocols. Polyclonal or monoclonal antibodies that are immunologically specific for the Arabidopsis EDR1 can be utilized for identifying and purifying EDR1 from Arabidopsis and other species. For example, antibodies may be utilized for affinity separation of proteins for which they are specific or to quantify the protein. Antibodies may also be used to immunoprecipitate proteins from a sample containing a mixture of proteins and other biological molecules.

IV. Use of EDR1 Nucleic Acids, EDR1 Proteins and Antibodies, edr1 Mutants, and Transgenic Plants

A. Uses of EDR1 Nucleic Acids.

EDR1 nucleic acids may be used for a variety of purposes in accordance with the present invention. DNA, RNA, or fragments thereof may be used as probes to detect the presence and/or expression of EDR1 genes. Methods in which EDR1 nucleic acids may be utilized as probes for such assays include, but are not limited to: (1) in situ hybridization; (2) Southern hybridization (3) Northern hybridization; and (4) assorted amplification reactions such as polymerase chain reactions (PCR).

The EDR1 nucleic acids of the invention may also be utilized as probes to identify related genes from other plant species. As is well known in the art, hybridization stringencies may be adjusted to allow hybridization of nucleic acid probes with complementary sequences of varying degrees of homology. As described above, EDR1 nucleic acids may be used to advantage to produce large quantities of substantially pure EDR1, or selected portions thereof. The EDR1 nucleic acids can be used to identify and isolate further members of this novel disease resistance signal transduction pathway in vivo. A yeast two hybrid system can be used to identify proteins that physically interact with the EDR1 protein, as well as isolate their nucleic acids. In this system, the sequence encoding the protein of interest is operably linked to the sequence encoding half of a activator protein. This construct is used to transform a yeast cell library which has been transformed with DNA constructs that contain the coding sequence for the other half of the activator protein operably linked to a random coding sequence from the organism of interest. When the protein made by the random coding sequence from the library interacts with the protein of interest, the two halves of the activator protein are physically associated and form a functional unit that activates the reporter gene. In accordance with the present invention, all or part of the Arabidopsis EDR1 coding sequence may be operably linked to the coding sequence of the first half of the activator, and the library of random coding sequences may be constructed with cDNA from Arabidopsis and operably linked to the coding sequence of the second half of the activator protein. Several activator protein/reporter genes are customarily used in the yeast two hybrid system. In a preferred embodiment, the bacterial repressor LexA DNA-binding domain and the Gal4 transcription activation domain fusion proteins associate to activate the LacZ reporter gene (see Clark et al., 1998, PNAS 95:5401–5406). Kits for the two hybrid system are also commercially available from Clontech, Palo Alto Calif., among others.

B. Uses of EDR1 Proteins and Antibodies:

The EDR1 proteins of the present invention can be used to identify molecules with binding affinity for EDR1, which are likely to be novel participants in this resistance pathway. In these assays, the known protein is allowed to form a physical interaction with the unknown binding molecule(s), often in a heterogenous solution of proteins. The known protein in complex with associated molecules is then isolated, and the nature of the associated protein(s) and/or other molecules is determined.

Antibodies that are immunologically specific for EDR1 may be utilized in affinity chromatography to isolate the EDR1 protein, to quantify the EDR1 protein utilizing techniques such as western blotting and ELISA, or to immuno-precipitate EDR1 from a sample containing a mixture of proteins and other biological materials. The immuno-precipitation of EDR1 is particularly advantageous when utilized to isolate affinity binding complexes of EDR1, as described above.

C. Uses of edr1 Mutants.

The edr1 mutants of the invention display enhanced disease resistance to plant pathogens of both fungal and bacterial origin, and therefore can be used to improve crop and horticultural plant species. The edr1 mutants are particularly resistant to powdery mildew. Such mutants will therefore be particularly useful when isolated from crop and horticultural varieties in which an infection by powdery mildew-inducing fungi, such as Erisyphe spp., Oidium spp. and Uncinula necator, results in loss. Plants species contemplated in regard to this invention include, but are not limited to: aster, barley, begonia, beet, cantaloupe, carrot, chrysanthemum, clover, corn, cucumber, delphinium, grape, lawn and turf grasses, lettuce, pea, peppermint, rice, rutabaga, sugar beet, tomatillo, tomato, turnip, wheat, and zinnia.

The edr1 mutants have a broad-based resistance to Erysiphe, also encompassing the species E. cruciferarum. It is therefore contemplated that the edr1 mutants will exhibit broad-spectrum resistance against a wide range of Erysiphe species and other members of Erysiphales. Such species include, but are not limited to, E. graminis, E. polygoni, E. betae, E. heraclei, E. pisi, E. trifolii, the Oidium species, particularly O. lycopersicon, and the Uncinula species, particularly U. necator. The mechanism of resistance involves the repression of fruiting body formation, and since pathogenic fungi in general have very similar methods infection, it is contemplated that these mutants will be more resistant to many forms of pathogenic fungi. Other fungal species considered in connection with the invention include, but are not limited to, biotrophic fungal species, such as those causing downy mildew and rust diseases.

The enhanced resistance exhibited by the mutants of the invention extends also to bacterial plant pathogens. The edr1 mutants exhibit increased resistance to Pseudomonas syringae and Pseudomonas syringae pv maculicola M2. This broad spectrum resistance to Pseudomonas strains is very likely to extend to all Pseudomonas species. The edr1 mutants are contemplated for use in providing resistance to all Pseudomonas species, including but not limited to, P. cichorii, P. coronafaciens, P. lacrymans, P. marginata and numerous P. syringae pathovars. It is contemplated that edr1 mutations will be selected from plant species that are susceptible to Pseudomonas infection: blueberry, english laurel, lilac, willow, apple, pear, raspberry, lettuce, oats, cucumber, gladiolus, bean, pea, cherry, maple, prune, plum, tomato, soybean, wheat, barley, rice and corn, among others.

The edr1 mutants exhibit a heightened induction of normal resistance pathways. It is therefore contemplated that these mutants will have enhanced resistance to a myriad of plant pathogens in addition to the specific fungal and bacterial species mentioned heretofore.

The edr1 mutants of the invention can be used to identify and isolate additional members of this disease resistance pathway. Mutations that, when combined with edr1, suppress the edr1 phenotype, are likely to interact directly with EDR1, or to compensate in some other way for the loss of EDR1 function.

E. Uses of EDR1 Transgenic Plants.

The transgenic plants of the invention are particularly useful in conferring the edr1 phenotype to many different plant species. In this manner, a host of plant species with enhanced disease resistance can be easily made, to be used as breeding lines or directly in commercial operations. Such plants can have uses as crop species, or for ornamental use.

A plant that has had functional EDR1 transgenically depleted will exhibit the same enhanced resistance as the edr1 mutants. It is therefore contemplated that transgenic edr1-phenotype plants will be used with the same aforementioned pathogens and plant species as the edr1 mutants. A transgenic approach is advantageous because it allows edr1-phenotype plants to be created quickly, without time-consuming mutant generation, selection, and back-crossing. Transgenically created edr1-phenotype plants have special utility in polyploid plants, such as wheat, where recessive mutations are difficult to detect.

A plant that has had functional EDR1 increased may have delayed senescence compared to wild-type plants. Plants with delayed senescence will be extremely valuable to agriculture and horticulture by allowing plants to flower, leaves to remain productive, and harvested fruits, vegetables and flowers to remain fresh for longer periods of time. It may also allow fruit with abscission zones such as tomato to accumulate sugars from a longer period of time.

The following examples are provided to describe the invention in greater detail. They are intended to illustrate, not to limit, the invention.

EXAMPLE 1 Isolation and Characterization of the edr1 Mutant in Arabidopsis

Methods

Bacterial and Fungal Strains and Media. Strain DC3000 of Pseudomonas syringae pv tomato was obtained from D. Cuppels (Agricultural Canada-Research Center, London, Ontario, Canada) and strain M4 of P. s. pv maculicola was provided by J. Dangl (University of North Carolina, Chapel Hill). Both P. syringae strains were cultured at 30° C. on either King's medium B (King et al., 1954, J. Lab. Clin. Med. 44:301–307) or trypticase soy agar (TSA; Becton Dickinson, Cockeysville, Md.) supplemented with 100 mg/L rifamycin (Sigma). Strain UCSC of Erysiphe cichoracearum was kindly provided by S. Sommerville (Carnegie Institute of Washington, Stanford, Calif.) and was maintained on Arabidopsis accession Columbia (Col-0) by brushing diseased plants onto new plants. Inoculated plants were maintained under a 14-hr day length at 22° C.

Seed Sources. Wild-type Arabidopsis thaliana ecotype Col-0 seed was obtained from B. J. Staskawicz (University of California, Berkeley). Mutagenized seed (M₂ generation) was obtained from Lehle Seeds (Round Rock, Tex.; fast-neutron mutagenized) or M. Estelle (Indiana University, Bloomington; ethyl methanesulfonate mutagenized and γ-irradiated). In all cases, M₁ generation seeds were mutagenized, planted and allowed to self-pollinate to generate the M₂ population. M₂ populations were bulked from approximately 500 M₁ plants. The edr1 mutant was isolated from the γ-irradiated population. Third and fourth generations (M₃ and M₄) of the edr1 mutant were used interchangeably for phenotypic analyses and crosses.

Arabidopsis Growth and Bacterial Inoculation. Arabidopsis seeds were sown in 4-inch-round pots filled with Perlite Plug Mix (Grace Sierra, Milpitas, Calif.). Pots were covered with 1.3-mm nylon mesh (window/door screen), and plants were allowed to grow through the screen. Seeded pots were covered and held at 4° C. for 3 days before being placed in growth rooms under a 9-hr day length (100 to 150 microE·m−2·sec⁻¹ of light) at 24° C. Covers were removed after the seeds sprouted and the first true leaves were emerging.

Adult plants (4 to 6 weeks after sowing) were inoculated by dipping whole rosettes in a suspension of 1×10⁹ colony-forming units of P. s. tomato DC3000 per ml suspended in 10 mM MgCl₂ supplemented with 0.025% (v/v) L77 Silwet (OSI Specialties, Danbury, Conn.). Inoculated plants were maintained for about 24 hr with humidity domes under growth conditions described above. Disease symptoms were scored 4 to 5 days after inoculation.

To monitor bacterial growth inside plant leaves, adult plants (4 to 6 weeks after sowing) were vacuum infiltrated with 1×10⁵ colony-forming units per ml of P. s. maculicola M4. Bacterial suspensions contained 0.01% L77 Silwet and 10 mM MgCl₂. At specific time points, samples were removed from rosette leaves using a number 2 cork borer (three discs per sample) and macerated in 200 μl of 10 mM MgCl₂. Dilutions were made in 10 mM MgCl₂ and plated on trypticase soy agar containing 100 mg/L rifamycin and incubated at 30° C. Colonies were counted 48 hr later.

E. cichozacearum Inoculation and Histology. E. cichoracearum actively growing on Col-0 plants (7–10 days post-inoculation) was used as an inoculum. To inoculate plants, diseased plants were used to brush healthy plants, thus passing spores onto the new plants.

Fungal structures and dead plant cells were stained by collecting leaves and boiling for 2 min in alcoholic lactophenol trypan blue (20 ml of ethanol, 10 ml of phenol, 10 ml of water, 10 ml of lactic acid (83%), and 10 mg of trypan blue). Stained leaves were cleared in chloral hydrate (2.5 g dissolved in 1 ml of water) overnight at room temperature (Koch and Slusarenko, 1990, Plant Cell, 2:437–445). Cleared leaves were mounted under coverslips in 50% glycerol.

Autofluorescence and callose were detected as described by Adam and Sommerville (1995, Plant J. 9:341–356). To observe all tissues, leaves were mounted under coverslips with 50% glycerol and observed with an Axiophot Microscope (Carl Zeiss, Oberkochen, Germany). Autofluorescence and callose fluorescence were analyzed using a 4′,6-diamidino-2-phenylindole filter setting.

Quantification of E. cichoracearum Growth. The percentage of germinating spores was determined 1 day after inoculation. Germination was defined as the presence of a germ tube. Hyphal length (3 days and 7 days post inoculation) and conidiophore number (7 days post inoculation) were obtained from a minimum of six trypan blue-stained leaves collected from separate experiments. Microscopic images (described above) were captured and digitized using a ZVS-3C75DE 3 CCD video camera (Carl Zeiss) and PowerTower Pro 180 computer (PowerComputing, Round Rock, Tex.). Digitized images were viewed and printed using Adobe Photoshop software (Adobe Systems, San Jose, Calif.). Hyphal length at 3 days post inoculation was measured on the printed images and converted to actual measurements by comparing to an image of a slide micrometer. To calculate conidiophores per millimeter of hyphae at 7 days post inoculation, hyphal length was estimated using a 50-mm grid on the printed image as described by Olson (1950, Trans. Am. Microscop. Soc. 69:272–279). Conidiophores on the printed image were counted directly. Fields with approximately equal hyphal density were chosen to assure equal sampling.

Analysis of Pathogenesis-Related Gene Expression. RNA was purified from frozen leaf tissue using a phenol-chloroform-guanidine hydrochloride extraction procedure (Logemann et al., 1987, Anal. Biochem. 163:16–20). RNA concentration was determined spectrophotometrically by absorbance at 260 nm. Twenty-five-microgram samples of total RNA were separated by electrophoresis through a formaldehyde agarose (1.5%) gel (Sambrook et al., 1989, supra). RNA was transferred from the gel to a nylon membrane and hybridized to ³²P-dATP-labeled DNA probes following the manufacturer's instructions (Hybond N, Amersham). Probes were generated using a Random Primed DNA labeling kit (Boehringer Mannheim). DNA templates for probes were generated by polymerase chain reaction amplification of Arabidopsis genomic DNA (BGL2, PR-5, and ubiquitin [UBQ5]) or amplification from a cDNA clone (PR-1; Uknes, et al., 1992, Plant Cell, 4:645–656) using published primers (Glazebrook et al., 1996, Genetics 143:973–982). Hybridization was quantified using a Molecular Dynamics (Sunnyvale, Calif.) PhosphorImager. Values for PR-1 and BGL2 hybridization were normalized for unequal loading using values obtained from the UBQ5 hybridization. Images were obtained by exposing the membrane to X-ray film (Fuji Film RX, Fisher Scientific).

Genetic Analysis. Arabidopsis mutant edr1 was crossed to accession Landsberg erecta (Ler). The F₁, F₂, and F₃ plants were scored for the mutant phenotype after dusting with E. cichoracearum spores. Resistant F₂ plants were selected for generation of F₃ families, which were used to confirm F₂ mutant phenotypes. DNA for analysis of molecular markers was collected from one or two inner rosette leaves of resistant F₂ plants using a hexadecyltri-methylammonium bromide (CTAB) extraction procedure (Bisgrove et al., 1994, Plant Cell, 6:927–933). Simple sequence length polymorphism (SSLP) and codominant amplified polymorphic sequence (CAPS) markers were amplified using the polymerase chain reaction (Konieczny and Ausubel, 1993, Plant J. 4:403–410; Bell and Ecker, 1994, Genomics 19:137–144). All primers for SSLP and CAPS markers were purchased from Research Genetics (Hunstville, Ala.). Amplified products were resolved on a 4% NuSieve gel (3:1 NuSieve:Seakem LE, FMC, Rockland, Me.).

Results

Isolation of Arabidopsis Mutants Resistant to Disease. Arabidopsis accession Columbia (Col-0) is susceptible to P. s. tomato DC3000. Disease symptoms develop on rosette leaves 4 to 5 days after inoculation and appear as gray lesions surrounded by chlorosis (Whalen et al., 1991, Plant Cell, 3:49–59). To identify Arabidopsis mutants with reduced susceptibility, we inoculated mutagenized Col-0 plants (M₂ generation) with P. s. tomato DC3000 and scored for disease lesion severity 4 to 5 days later. Plants were inoculated with a high dose of P. s. tomato DC3000 (1×10⁹ colony forming units per ml), facilitating the identification of living resistant plants because at this concentration susceptible plants frequently died. Living plants displaying a decrease in the severity of disease symptoms were selected for further analysis. Reduced disease symptoms included fewer leaves showing disease, smaller lesions, and a lack of lesions on inner-rosette leaves. Approximately 25,000 mutagenized Col-0 plants were screened, and 78 putative mutants were selected. The mutant phenotype of decreased disease symptoms was found to be heritable in 36 of the 78 plants selected.

To determine whether reduced symptoms correlated with reduced bacterial growth, we quantified bacterial numbers in leaves over a 4-day period. Of the 36 mutants, 25 showed a reduction in bacterial growth in the leaves as compared to wild-type Col-0 plants.

To eliminate mutants that were constitutively expressing SAR, we analyzed expression of the PR-1 gene in uninoculated plants. PR-1 gene expression was assayed using RNA gel blot analysis. Of 19 mutants analyzed (six were not tested), six displayed strong expression of PR-1, seven displayed weak expression, and six did not have detectable expression of PR-1. The latter six mutants represent a novel class as they are less susceptible to a virulent pathogen by a mechanism independent of constitutive expression of SAR. These mutants have been termed enhanced disease resistant (edr).

To determine whether any of the edr mutants displayed broad spectrum disease resistance, we tested them for resistance to E. cichoracearum, causal agent of powdery mildew. Arabidopsis accession Col-0 is susceptible to the UCSC strain of E. cichoracearum, developing the macroscopic disease symptoms of powdery mildew (a white powder resulting from production of asexual spores; Adam and Somerville, 1996, supra) on the leaves 7–10 days after inoculation. One of the six edr mutants displayed resistance to E. cichoracearum, developing almost no visible powder. We performed a phenotypic and genetic analysis of this mutant, which we have designated edr1.

Decreased Susceptibility of edr1 Plants to Bacterial Pathogens. Decreased susceptibility to P. s. tomato DC3000 was a criterion for selecting the edr mutants. Edr1 plants displayed fewer disease lesions than wild-type Col-0 plants after inoculation with P. s. tomato. At 2 days post inoculation, the level of P. s. tomato DC3000 in edr1 leaves was significantly less than level of P. s. tomato DC 3000 in wild-type Col-0 leaves FIG. 1A; t=3.01, P=0.0395). While the difference in bacterial growth between edr1 and Col-0 plants was small, the difference in disease lesion development was more striking. These results suggested a relationship between bacterial growth from 0–2 days post inoculation and the severity of disease lesions.

To determine whether the edr1 mutant was less susceptible to a second bacterial pathogen, we inoculated edr1 and wild-type Col-0 plants with P. s. maculicola strain M4 and examined both lesion development and bacterial growth in plant leaves over 4 days. Pseudomonas s. maculicola M4 is virulent on Col-0 causing disease symptoms similar to those of P. s. tomato DC3000 (gray lesions surrounded by chlorosis). The edr1 plants developed less severe disease symptoms than wild-type Col-0 after inoculation with P. s. maculicola M4, suggesting decreased susceptibility to P. s. maculicola M4. Analysis of P. s. maculicola M4 growth in edr1 plants also indicated decreased susceptibility (FIG. 1B), however this difference was not statistically significant (t=1.97, P=0.12).

E. cichoracearum is arrested at a late stage of the infection process in edr1 plants. The infection process of E. cichoracearum on Arabidopsis is known. Spores first produce appressorial germ tubes that penetrate the underlying epidermal cells. Inside the epidermal cells the fungus forms a haustorium, which is a bag-like invagination surrounded by host cell plasma membrane. Fungal development then proceeds via formation of secondary hyphae and haustoria and terminates with formation of conidiophores (stalks of asexual spores) 5 to 7 days after infection. It is these conidiophores that produce the “powdery” appearance for which the disease is named.

Approximately 7 days after inoculation with asexual spores of E. cichoracearum, wild-type Arabidopsis plants displayed abundant conidiophores (visible white powder) on mature plant leaves. The edr1 plants displayed strong disease resistance to E. cichoracearum. Starting 6 days post inoculation, the mature leaves of edr1 plants became slightly chlorotic then developed distinct necrotic and collapsed regions. Over the next 3 days the necrosis spread to consume large portions of the leaf. During this same time period, wild-type Col-0 leaves displayed abundant conidiophores with some chlorosis but no necrosis. Visible necrosis in edr1 plants began just prior to the development of visible powder on wild-type Col-0 plants. The edr1 mutant developed only small scattered patches of powder.

To determine the stage of fungal development that was affected on edr1 plants, infected leaves at various time points were stained with trypan blue, which detects both fungal structures and dead plant cells (Koch and Slusarenko, 1990, Plant Cell 2:437–445). As shown in Table 2, on both Col-0 and edr1 leaves, approximately 60% of the spores developed appressorial germ tubes 1 day after inoculation. By 3 days after inoculation, E. cichoracearum spores developed extensive branched hyphae with secondary germ tubes that invaded underlying epidermal cells. The average length of hyphae did not differ between germlings on edr1 leaves and Col-0 leaves (Table 2).

TABLE 2 Erysiphe development on wild-type Col-O and edrl leaves. stage of development Col-0 edrl germination 65.3% (49) 66.0% (50) hyphal length^(b) 1.99 ± 0.2 mm (16) 1.86 ± 0.2 mm (18) conidiophores/mm 2.47 ± 0.34 (7) 0.38 ± 0.12 (12) hyphae^(c) ^(a)Asexual spore germination measured 1 day post-inoculation. Values are expressed as the mean ± SE; (n) = number of germlings.

By 5 days post inoculation E. cichoracearum developed extensive hyphal growth that nearly covered the leaf surface on both edr1 and wild-type Col-0 plants. By day 7, E. cichoracearum developed abundant conidiophores on wild-type Col-0 plants; however, these structures were severely reduced in number on edr1 leaves (Table 2). The conidiophores that were present on edr1 leaves often were not septated and appeared to be under-developed compared to those on wild-type Col-0 leaves at the same time point. These observations indicate E. cichoracearum development is arrested just prior to formation of conidiophores, a relatively late stage in the infection process.

Defense Responses Are More Strongly Induced In edr1 Plants. The necrotic patches observed on edr1 plants after infection with E. cichoracearum indicated that cell death was occurring. Therefore, we determined whether edr1 plants displayed microscopic patches of dead cells prior to pathogen exposure as has been reported for mlo and lesions simulating disease (lsd) mutants. Dead cells were visualized using trypan blue staining. No difference between edr1 and wild-type plants was observed prior to pathogen exposure. Five days after inoculation with E. cichoracearum, both edr1 and wild-type Col-0 plants displayed small scattered groups of dead cells that did not correlate with presence of fungal hyphae. Leaves from edr1 plants, however, contained large clusters of dead mesophyll cells (more than 30 cells) that were invariably associated with areas of dense hyphal growth. Large clusters of dead cells were not observed in wild-type Col-0 leaves.

Plant cells undergoing an HR accumulate callose and autofluorescent compounds in the cell wall. To determine whether the necrosis observed in edr1 plants shared the biochemical properties of an HR, we assayed infected leaves for deposition of autofluorescent compounds and for callose. Both wild-type Col-0 and edr1 plants displayed punctate staining of callose in the cell walls of epidermal cells approximately 3 days post inoculation; however, only edr1 plants showed callose staining in large clumps of mesophyll cells. The bright punctate staining observed in epidermal cells of both Col-0 and edr1 plants is absent in noninoculated plant leaves and probably represents a collar of callose-containing plant material. It has been shown that susceptible and resistant plants respond to fungal penetration by generating a papilla at the infection site.

In susceptible plants, the fungus penetrates through the papillae that subsequently becomes a collar around the penetration peg. Callose deposition in the mesophyll cells of edr1 leaves is evident 3 days after inoculation with E. cichoracearum, which is prior to the appearance of dead cells. The pattern of autofluorescence was similar to that observed for callose. Autofluorescing mesophyll cells accumulated in edr1 leaves beginning 3 days post inoculation. Col-0 leaves showed only scattered epidermal cells autofluorescing at the same time point.

Analysis of PR Gene Expression. One of the criteria used to identify the edr1 mutant was the lack of constitutive PR-1 gene expression. It was possible, however, that the enhanced resistance of edr1 was mediated by a more rapid or stronger induction of SAR, or of SAR-associated genes other than PR-1. Therefore, we used RNA gel blot analysis to assay for expression of three SAR-associated genes during infection by E. cichoracearum.

Little to no PR-1 and BGL2 mRNA was detectable prior to inoculation, or 1 day after infection. By 3 days after infection, significant levels of PR-1 and BGL2 were observed in both wild type and edr1 plants. We quantified the levels of mRNA detected by using a PhosphorImager. The level of PR-1 message in edr1 leaves at day 3 was approximately four times higher than in Col-0 leaves. PR-1 and BGL2 transcript levels increased at days 5 and 7 after infection, but the relative difference between edr1 and wild-type plants was less. By day 7, PR-1 levels were higher in wild-type Col-0 than in edr1 -plants. Analysis of BGL2 and PR-5 transcript levels also revealed a small but reproducible increase in edr1 plants relative to wild type Col-0 on days 3 and 5 after inoculation.

Genetic Analysis of edr1. To determine the inheritance of the enhanced resistance phenotype, the edr1 mutant was crossed with Arabidopsis accession Landsberg erecta (Ler), which is susceptible E. cichoracearum. The F₂ progeny were inoculated with E. cichoracearum conidia and scored 7–9 days later for development of necrotic lesions and lack of visible powdery mildew. These two traits co-segregated, and behaved as a recessive mutation, producing approximately a 1:3 ratio of resistant-to-susceptible plants (85:266; X²=0.115; P>0.1).

To obtain a chromosomal map position for the mutation in edr1 plants, a total of 1223 F₂ plants from the Ler cross were scored for E. cichoracearum resistance and 235 plants displaying resistance to E. cichoracearum were selected for mapping. DNA was isolated from the resistant F₂ plants and analyzed for linkage to SSLP and CAPS markers (Konieczny and Ausubel, 1993, supra; Bell and Ecker, 1994, supra). The edr1 mutation mapped 3.2 centiMorgans centromeric from the SSLP marker ATEAT1 (15 recombinant chromosomes) and 0.85 centiMorgans telomeric from the CAPS marker NCC1 (4 recombinant chromosomes) on chromosome 1.

Discussion

The edr1 mutant displays enhanced resistance to powdery mildew, but does not constitutively express pathogenesis related genes, such as PR-1 and BGL2. The latter observation indicates resistance is being conferred by a mechanism that differs from previously described Arabidopsis disease resistant mutants. Our data show that multiple defense responses are induced more rapidly in edr1 plants than in wild-type plants when infected with a virulent strain of powdery mildew. These observations suggest that the edr1 mutation leads to a “hair trigger” inducibility of these responses.

We obtained the edr1 mutant by screening for plants that displayed enhanced resistance to the bacterial pathogen P. s. tomato DC3000, suggesting that the edr1 mutation also enables a more rapid defense response against bacteria. However, the resistance to P. s. tomato DC3000 was variable. The edr1 mutant also displayed variable resistance to a second strain of P. syringae, P. s. pv maculicola M2. These observations suggest that edr1-mediated resistance to P. syringae may be influenced by environmental factors.

The difference in effect of the edr1 mutation on P. syringae infection compared to E. cichoracearum might be related to the different modes of infection of these pathogens. P. syringae colonizes the intercellular spaces of the leaf mesophyll, reaching maximum population levels within 2 to 3 days after infection. In contrast, E. cichoracearum remains on the leaf surface and does not produce spores until 6 to 7 days after infection.

To further evaluate the spectrum of resistance conferred by the edr1 mutation, the mutant was challenged with additional pathogens. The edr1 mutant was found to be resistant to a second species of Erysiphe, E. cruciferarum strain UEA1. This pathogen induced a resistance phenotype essentially the same as that induced by E. cichoracearum, including mesophyll cell death associated with a dramatic decrease in conidiophore production. This result suggests the edr1 mutation confers a broad-spectrum rather than race-specific resistance against powdery mildew.

Resistance to E. cichoracearum in edr1 plants is manifested at a relatively late stage in the infection. Erysiphe cichoracearum spores germinated on the leaf surface and developed extensive networks of secondary hyphae on both edr1 and wild-type Col-0 plants. Asexual reproduction was dramatically reduced on edr1 plants; both the number of conidiophores formed as well as the number of conidia that make up each conidiophore were decreased. These observations suggest that the edr1 resistance response affects the fungus primarily after onset of conidiophore formation at day 4.

Consistent with the observed effect on fungus development, we did not detect enhanced defense responses in edr1 plants until 3 days after infection with E. cichoracearum. The earliest response detected was deposition of callose and autofluorescent compounds in epidermal cells and underlying mesophyll cells. We also observed a slightly enhanced expression of PR genes at day 3; however, cell death was not observed until 5 days after inoculation.

In response to fungal infection, the defense mechanisms observed in edr1 plants are slow compared to that conferred by most classical disease resistance genes. For example, barley plants containing the Mla1 gene induce a single cell HR within 14 hr of infection by an avirulent strain of Erysiphe graminis f.sp. hordei, preventing the fungus from forming secondary hyphae (et al., 1995, Plant J. 7:959–968). Not all powdery mildew resistance genes confer a rapid HR, however. The resistance phenotype of edr1 plants to E. cichoracearum is similar to the phenotypes conferred by the Pm2 and pm5 genes of wheat, and the Mla3 and Mla7 genes of barley. These resistance genes affect powdery mildew growth after the development of secondary hyphae, but before conidiophore production, and are associated with the accumulation of large masses of dead mesophyll cells (Hyde and Colhoun, 1975, Phytopath. Z. 82:185–206; Boyd, et al., 1995, supra). In addition, plants with rapidly acting resistance genes occasionally allow fungal germlings to form secondary hyphae. Growth of such escapees is usually halted prior to conidiophore formation and is associated with mesophyll cell death (Hyde and Colhoun, 1975, supra).

The edr1 resistance phenotype shares some attributes with resistance mediated by the mlo mutation of barley. The mlo mutation is recessive and confers resistance to multiple races of E. g. hordei, but has no apparent effect on other pathogen species tested, such as Puccinia hordei, the causative agent of rust on barley (Jorgensen, 1992, supra; Wolter, et al., 1993, supra). Similarly, edr1 plants showed clear resistance to two species of powdery mildew, but variable resistance to bacterial pathogens. Unlike edr1, however, mlo resistance is associated with the formation of callose rich papillae that are thought to block penetration of the fungus into the initially infected epidermal cell (Aist et al., 1988, Physiol. Molec. Plant Pathol. 33:17–32; Wolter, et al., 1993, supra); secondary hyphae very rarely form on mlo plants. The edr1 mutation does not map to the same location as the Mlo-like Arabidopsis genes identified previously (Büschges, et al., 1997, Cell, 88:695–705).

EXAMPLE 2 Isolation and Analysis of the EDR1 Gene

Isolation of the EDR1 gene. The edr1 mutation was located on the genetic map of Arabidopsis by genetic linkage analysis (see Example 1). After identifying closely linked molecular markers, two overlapping bacterial artificial chromosome (BAC) clones were identified that genetically span the region containing edr1. EDR1 was therefore contained on one of these two BAC clones, F22013 and F7G19, which are publicly available clones generated as part of the ongoing Arabidopsis genome project. The complete DNA sequence of these two clones is available from the Genbank DNA database. Using this sequence information, additional molecular markers were generated that localized the EDR1 gene to an approximately 100 kilobase pair interval, most of which was contained on BAC clone F22013. Analysis of the DNA sequence in this interval revealed 25 potential protein coding genes. To determine which of these 25 genes encoded EDR1, candidate genes from our edr1 mutant were sequenced with the reasoning that the EDR1 gene should contain an alteration in its DNA sequence in the edr1 mutant plant. Candidate genes were amplified from the edr1 mutant using the polymerase chain reaction (PCR). DNA sequences of PCR products were determined using an ABI Dye Terminator FS kit protocol (Perkin-Elmer, Foster City, Calif.) on an ABI Prism 377 DNA sequencer.

Candidates were chosen based on the probability that mutations in such genes could lead to the observed edr1 phenotype. In particular, genes known to play a role in stress responses (e.g. superoxide dismutase) or in signal transduction (e.g. protein kinases and transcription factors) were focused on. Upon sequencing candidate gene F22013.21, which had similarity to MAP3 kinases (also known as “mitogen activated protein kinase kinase kinase”), a single nucleotide difference between the edr1 mutant and wild-type Arabidopsis was discovered. This gene was sequenced again from wild-type Arabidopsis plants to insure this nucleotide difference was correct. This nucleotide change produces a premature stop codon (codon 392 (TAC) is converted to a TAG (stop) codon), thus eliminating the C-terminal half of the protein, including the entire putative protein kinase domain (see SEQ ID NO:1). Such a mutation would be expected to render the EDR1 protein non-functional, which is consistent with the recessive nature of the edr1 mutation. Because this nucleotide change co-segregates with the edr1 phenotype, it is very likely that this MAP3 kinase represents EDR1. To prove this, a wild-type copy of the EDR1 gene was transformed into an edr1 mutant Arabidopsis plant using Agrobacterium-mediated transformation. Four out of five independent transgenic lines showed a restoration of a wild-type phenotype, indicating the indentified MAP3 kinase gene could rescue the edr1 mutant phenotype. Henceforth, this MAP3 kinase is referred to as the EDR1 protein.

Structural Analysis of the Predicted EDR1 Protein. The EDR1 protein sequence (SEQ ID NO:2) contains high similarity to a large number of protein kinases, which are proteins that can catalyze the addition of phosphate groups to other proteins. Many protein kinases are known to participate in signal relays, passing information from outside the cell to other sites within the cell (“signal transduction”). One of the proteins most similar to EDR1 is another Arabidopsis protein called CTR1 (SEQ ID NO:3). The similarity is highest in the putative kinase domain, but extends to other regions of the protein as well (FIG. 2). This similarity is informative, as a considerable amount is known about CTR1. Loss of function mutations in CTR1 result in induction of ethylene-induced responses. In other words, plants with null mutations in CTR1 behave as if they are being exposed to high levels of ethylene all the time. The CTRL protein functions to repress (i.e. keep off) these responses in the absence of ethylene. In the presence of ethylene, the CTR1 protein is inactivated, leading to the induction of these responses. The CTR1 protein is thus described as a negative regulator of the ethylene response pathway. The EDR1 protein may by analogy function as a negative regulator of specific defense response pathways. In the absence of functional EDR1 protein, these pathways are more easily induced by pathogens, leading to enhanced disease resistance.

The CTR1 protein has been shown to interact with a second protein known as ETR1, which is a receptor for the ethylene molecule. This interaction indicates that CTRL functions near the beginning of the signal relay between perception of ethylene and the activation of ethylene responses. The similarity between CTR1 and EDR1 suggests that EDR1 may also function near the beginning of a signal relay, perhaps activated by a pathogen molecule.

Homologs of EDR1 exist in Crop Species. The Arabidopsis EDR1 sequence has been used to identify homologs in rice and barley, and can be used to identify homologs in other crop plants. Once these homologous genes are identified they can be inactivated, thus creating edr1-like mutants that have enhanced disease resistance. A search of the Genbank DNA, protein, and expressed sequence tag (EST) databases reveals several strongly homologous genes. Although many genes show similarity to the kinase domain encoding portion of EDR1, one gene from tomato called TCTR2 (SEQ ID NO:4) shows extensive homology throughout the protein-coding region (FIG. 3), indicating that this gene encodes the tomato version of EDR1. Alignment of EDR1 and TCTR2 reveals numerous regions where the amino acid sequences are identical. Such regions may be used to design PCR primers to enable amplification of EDR1 homologs from other plant species.

In addition to TCTR2, EDR1 showed high similarity to an EST sequence from rice. Because EST sequences represent only partial sequences of the corresponding cDNA clones, this cDNA clone was obtained and the complete DNA sequence determined (SEQ ID NO:5). The rice EDR1 protein sequence (SEQ ID NO:6) is aligned with EDR1, TCTR2, and CTR1 in FIG. 4. The high degree of similarity between EDR1 and the protein encoded by the rice cDNA indicates that this cDNA corresponds to the rice version of EDR1. The protein sequence encoded by the rice cDNA is more similar to EDR1 and TCTR2 than any other sequences in the public databases, including CTR1 (Table 1).

The high degree of similarity between Arabidopsis EDR1, TCTR2, and rice EDR1 indicates that the EDR1 gene is well conserved among both monocots and dicots, which in turn suggests that it may function in a similar manner in all flowering plants. In addition, this high degree of conservation indicates that it will be straightforward to isolate EDR1 homologs from any plant species by homology-based approaches. For example, PCR-primers derived from regions that are identical in Arabidopsis, tomato and rice, but that differ from the analogous region of CTR1, should amplify EDR1 homologs from most flowering plant species. Two such regions are indicated in FIG. 4 (SEQ ID NOS: 7 and 8). Degenerate primers corresponding to these regions were used to successfully amplify an EDR1 homolog from barley (SEQ ID NO:9).

The present invention is not limited to the embodiments described and exemplified above, but is capable of variation and modification without departure from the scope of the appended claims. 

1. An isolated nucleic acid molecule comprising a nucleotide sequence encoding a polypeptide sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 6, and SEQ ID NO:
 10. 2. The nucleic acid molecule of claim 1, wherein the nucleotide sequence encodes SEQ ID NO:
 2. 3. The nucleic acid molecule of claim 2 wherein the nucleotide sequence is SEQ ID NO:
 1. 4. A vector comprising the nucleic acid molecule of claim
 1. 5. An isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: a) the nucleotide sequence of SEQ ID NO: 1; b) a nucleotide sequence encoding SEQ ID NO: 2; c) a nucleotide sequence encoding SEQ ID NO: 6; d) a nucleotide sequence encoding SEQ ID NO: 10 e) the nucleotide sequence of SEQ ID NO: 5; and f) the nucleotide sequence of SEQ ID NO:
 9. 6. A vector comprising the nucleic acid molecule of claim
 5. 